|
| Status |
Public on Dec 31, 2013 |
| Title |
DLD1-siRNA treated replicate2 |
| Sample type |
RNA |
| |
|
| Source name |
colorectal cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DLD1
treatment: siRNA beta-catenin
|
| Treatment protocol |
DLD1 and SW480 cells were harvested 48h after siRNA transfection
|
| Growth protocol |
The colon carcinoma cell lines DLD1 and SW480 were obtained from ATCC (Manassas, VA, USA) and were cultured in DMEM medium supplemented with 10% calf serum (PAA, Pasching, Austria). Short interfering RNAs targeting β-catenin (cat. no. D-003482-04) and β-Galactosidase (cat. no. D-012539-01) were purchased from Dharmacon (Lafayette, CO, USA) as siGenome siRNAs. Cells were transfected with these siRNAs using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol method
|
| Label |
biotin
|
| Label protocol |
Affymentrix kits for 3'IVT cDNAsynthesis, amplification and labeling
|
| |
|
| Hybridization protocol |
Fluidics station FS450
|
| Scan protocol |
Affymetrix GeneChip Scanner 3000
|
| Description |
colorectal cancer cell line, siRNA against beta-catenin
|
| Data processing |
The software package R (version 2.14.1) was used for the statistical analysis of the microarray data. Microarray data were preprocessed using the rma function from the R package “affy”. Two sets with different cell lines(DLD1 and SW480) were normalized separately. The function nsFilter from the package 'genefilter' was used to exclude all probeset that were not associated with a gene name.
|
| |
|
| Submission date |
Feb 05, 2013 |
| Last update date |
Dec 31, 2013 |
| Contact name |
Stefan Krebs |
| E-mail(s) |
krebs-st@lmb.uni-muenchen.de
|
| Phone |
0049-89-2180 76715
|
| Organization name |
Ludwig-Maximilian University
|
| Department |
Gene Center
|
| Lab |
Lafuga Genomics
|
| Street address |
Feodor-Lynen-Str. 25
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE44097 |
β-catenin target genes in colorectal carcinoma cell lines with deregulated Wnt/β-catenin signaling |
|
